Re: [AMBER] Stability MMPBSA

From: Kenneth Huang <>
Date: Mon, 30 Mar 2015 22:47:59 -0400


I haven't had a chance to run your files yet, but a useful tip when MMPBSA
crashes without giving an explicit error message as in this case, it's a
good idea to check the mdout file, since it should give you a much more
detailed error message than just where it's failing.My best guess is that
there's a bad atom mismatch, just based on the numbers in your topologies.



On Mon, Mar 30, 2015 at 9:44 PM, Parker de Waal <>

> Hi Everyone,
> I’m trying to perform alanine scanning on a GPCR in an explicit POPC
> membrane to assess energy contribution to protein stability.
> Unfortunately, each time I try to run the program the following
> error occurs:
> For input I am using:
> -sp 033015.prmtop (solvent complex in membrane)
> -cp proteinOnly.prmtop (protein only)
> -y (traj)
> -mc 40.prmtop (residue 40 mutated to ala)
> I’ve upload my input files to dropbox and they can be found here:
> Any insight would be truly appreciated.
> Best,
> Parker
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Received on Mon Mar 30 2015 - 20:00:02 PDT
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